-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_9032610-9208121

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_6-snap.2006-T1
Valid prediction for snap_scaffold_6-snap.2010-T1
Valid prediction for GeneMark_model.26240_t
Valid prediction for pasa_asmbl_47134.p1
Valid prediction for snap_scaffold_6-snap.2032-T1
Valid prediction for pasa_asmbl_47141.p1
Valid prediction for GeneMark_model.26248_t
Valid prediction for GlimmerHMM_glimmerT_15590-T1
Valid prediction for CodingQuarry_transcript_55019-T1
Valid prediction for snap_scaffold_6-snap.2025-T1
Valid prediction for pasa_asmbl_47160.p1
Valid prediction for GlimmerHMM_glimmerT_15576-T1
Valid prediction for HiQ_model.g10398.t1
Valid prediction for snap_scaffold_6-snap.2005-T1
Couldn't classify 22626, 22649
Couldn't classify 23725, 23870
Sorry, prediction pasa_asmbl_47948.p2 fails validation.
(TCC)	 CC	22626-22649	GT	AGG
(AGT)	 AG	23170-23309	GT	GGG
(GGT)	 AG	23406-23575	GT	AGG
(ACA)	 AG	23725-23870	AC	CCA
-recovered pasa_asmbl_47948.p2, internal, 23170, 23309
-recovered pasa_asmbl_47948.p2, internal, 23406, 23575
Valid prediction for pasa_asmbl_47135.p1
Valid prediction for snap_scaffold_6-snap.2031-T1
Valid prediction for snap_scaffold_6-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_15580-T1
Couldn't classify 25917, 25979
Couldn't classify 27046, 27087
Sorry, prediction pasa_asmbl_47129.p1 fails validation.
(GAT)	 TG	25917-25979	GT	AGG
(ACG)	 AG	26129-26263	GT	AGG
(TTT)	 AG	26454-26606	GT	ACG
(AAC)	 AG	26749-26907	GC	AGG
(GTC)	 AG	27046-27087	AC	ACA
-recovered pasa_asmbl_47129.p1, internal, 26129, 26263
-recovered pasa_asmbl_47129.p1, internal, 26454, 26606
-recovered pasa_asmbl_47129.p1, internal, 26749, 26907
Valid prediction for pasa_asmbl_47150.p1
Valid prediction for GeneMark_model.26229_t
Valid prediction for snap_scaffold_6-snap.2019-T1
Valid prediction for snap_scaffold_6-snap.2021-T1
Valid prediction for HiQ_model.g10402.t1
Valid prediction for pasa_asmbl_47159.p1
Valid prediction for GeneMark_model.26252_t
Valid prediction for GeneMark_model.26239_t
Valid prediction for GlimmerHMM_glimmerT_15593-T1
Valid prediction for GeneMark_model.26235_t
Valid prediction for snap_scaffold_6-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_15595-T1
Valid prediction for snap_scaffold_6-snap.2013-T1
Valid prediction for HiQ_model.g10396.t1
Valid prediction for GlimmerHMM_glimmerT_15585-T1
Valid prediction for HiQ_model.g10406.t1
Valid prediction for GlimmerHMM_glimmerT_15588-T1
Valid prediction for GeneMark_model.26245_t
Valid prediction for CodingQuarry_transcript_55010-T1
Valid prediction for HiQ_model.g10409.t1
Valid prediction for HiQ_model.g10407.t1
Valid prediction for GlimmerHMM_glimmerT_15581-T1
Valid prediction for CodingQuarry_transcript_55018-T1
Valid prediction for GeneMark_model.26255_t
Valid prediction for GeneMark_model.26237_t
Valid prediction for GeneMark_model.26244_t
Valid prediction for Augustus_model.g10394.t1
Valid prediction for CodingQuarry_transcript_55014-T1
Valid prediction for GeneMark_model.26227_t
Valid prediction for snap_scaffold_6-snap.2014-T1
Valid prediction for HiQ_model.g10400.t1
Valid prediction for GeneMark_model.26236_t
Valid prediction for snap_scaffold_6-snap.2008-T1
Valid prediction for GlimmerHMM_glimmerT_15574-T1
Valid prediction for Augustus_model.g10395.t1
Valid prediction for snap_scaffold_6-snap.2017-T1
Valid prediction for snap_scaffold_6-snap.2009-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15583-T1
Valid prediction for GlimmerHMM_glimmerT_15594-T1
Valid prediction for snap_scaffold_6-snap.2024-T1
Valid prediction for GlimmerHMM_glimmerT_15596-T1
Valid prediction for GlimmerHMM_glimmerT_15577-T1
Valid prediction for GeneMark_model.26253_t
Valid prediction for snap_scaffold_6-snap.2026-T1
Valid prediction for GeneMark_model.26247_t
Valid prediction for GlimmerHMM_glimmerT_15578-T1
Valid prediction for CodingQuarry_transcript_55011-T1
Valid prediction for Augustus_model.g10392.t1
Valid prediction for GeneMark_model.26242_t
Valid prediction for Augustus_model.g10391.t1
Valid prediction for GeneMark_model.26233_t
Valid prediction for Augustus_model.g10410.t1
Valid prediction for snap_scaffold_6-snap.2016-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.26225_t
Couldn't classify 60742, 60958
Sorry, prediction pasa_asmbl_47137.p1 fails validation.
(GTT)	 GT	60742-60958	GT	GAG
(CAA)	 AG	61187-61256	GT	AGG
(GTT)	 AG	63404-63536	GT	AGG
(GTG)	 AG	64598-64672	GT	GGG
(GCC)	 AG	65634-65787	GT	AAG
(CAG)	 AG	65963-66044	GT	AGG
(CCT)	 AG	66160-66297	GT	AGG
(GCC)	 AG	66731-66887	GT	AGG
(ATA)	 AG	67293-67399	GT	CTG
(GTA)	 AG	67771-67900	GT	AGG
(GCC)	 AG	68426-68615	GT	AAG
(CCA)	 AG	68728-68920	GT	AGG
(GCT)	 AG	69318-69483	GA	AGG
-recovered pasa_asmbl_47137.p1, terminal, 69318, 69483
-recovered pasa_asmbl_47137.p1, internal, 61187, 61256
-recovered pasa_asmbl_47137.p1, internal, 63404, 63536
-recovered pasa_asmbl_47137.p1, internal, 64598, 64672
-recovered pasa_asmbl_47137.p1, internal, 65634, 65787
-recovered pasa_asmbl_47137.p1, internal, 65963, 66044
-recovered pasa_asmbl_47137.p1, internal, 66160, 66297
-recovered pasa_asmbl_47137.p1, internal, 66731, 66887
-recovered pasa_asmbl_47137.p1, internal, 67293, 67399
-recovered pasa_asmbl_47137.p1, internal, 67771, 67900
-recovered pasa_asmbl_47137.p1, internal, 68426, 68615
-recovered pasa_asmbl_47137.p1, internal, 68728, 68920
Couldn't classify 27145, 27339
Sorry, prediction pasa_asmbl_47131.p1 fails validation.
(CGG)	 AC	27145-27339	GT	AGG
(AAC)	 AG	27441-27584	GT	TGG
(GCT)	 AG	27705-27836	GT	AGG
(AGT)	 AG	28061-28075	GT	AGG
(AGG)	 AG	28538-28663	GC	AGG
(GAA)	 AG	28757-28846	GT	AGG
(GCC)	 AG	28937-29173	GT	AGG
(ATC)	 AG	29306-29449	GT	AGG
(GGC)	 AG	29584-29690	GT	AGG
(GTG)	 AG	29792-29965	GT	CGG
(GAA)	 AG	30503-30545	AG	GAA
-recovered pasa_asmbl_47131.p1, terminal, 30503, 30545
-recovered pasa_asmbl_47131.p1, internal, 27441, 27584
-recovered pasa_asmbl_47131.p1, internal, 27705, 27836
-recovered pasa_asmbl_47131.p1, internal, 28061, 28075
-recovered pasa_asmbl_47131.p1, internal, 28538, 28663
-recovered pasa_asmbl_47131.p1, internal, 28757, 28846
-recovered pasa_asmbl_47131.p1, internal, 28937, 29173
-recovered pasa_asmbl_47131.p1, internal, 29306, 29449
-recovered pasa_asmbl_47131.p1, internal, 29584, 29690
-recovered pasa_asmbl_47131.p1, internal, 29792, 29965
Valid prediction for GeneMark_model.26231_t

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GeneMark_model.26230_t
Valid prediction for GeneMark_model.26238_t
Valid prediction for snap_scaffold_6-snap.2018-T1
Valid prediction for GlimmerHMM_glimmerT_15579-T1
Valid prediction for CodingQuarry_transcript_55017-T1
Valid prediction for GeneMark_model.26228_t
Valid prediction for CodingQuarry_transcript_55012-T1
Valid prediction for snap_scaffold_6-snap.2034-T1
Valid prediction for Augustus_model.g10403.t1
Valid prediction for GlimmerHMM_glimmerT_15598-T1
Valid prediction for snap_scaffold_6-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_15592-T1
Valid prediction for GlimmerHMM_glimmerT_15591-T1
Valid prediction for snap_scaffold_6-snap.2033-T1
Valid prediction for snap_scaffold_6-snap.2015-T1
Valid prediction for snap_scaffold_6-snap.2029-T1
Valid prediction for Augustus_model.g10393.t1
Valid prediction for GlimmerHMM_glimmerT_15584-T1
Couldn't classify 30087, 30246
Couldn't classify 30295, 30998
Sorry, prediction CodingQuarry_transcript_55020-T1 fails validation.
(ATG)	 CC	29181-29296	GT	AAG
(GCC)	 AG	29751-29916	GT	AGG
(GTT)	 AG	30087-30246	AC	CAA
(GCC)	 CA	30295-30998	GT	AGG
(ACA)	 AG	31657-31842	GT	AGG
(ACG)	 AG	31936-32067	GT	AGG
(TTT)	 AG	32150-32210	GT	AGG
(AGA)	 AG	32299-32798	GA	GAG
-recovered CodingQuarry_transcript_55020-T1, initial, 29181, 29296
-recovered CodingQuarry_transcript_55020-T1, terminal, 32299, 32798
-recovered CodingQuarry_transcript_55020-T1, internal, 29751, 29916
-recovered CodingQuarry_transcript_55020-T1, internal, 31657, 31842
-recovered CodingQuarry_transcript_55020-T1, internal, 31936, 32067
-recovered CodingQuarry_transcript_55020-T1, internal, 32150, 32210
Valid prediction for snap_scaffold_6-snap.2028-T1
Valid prediction for GeneMark_model.26234_t
Valid prediction for snap_scaffold_6-snap.2020-T1
Valid prediction for GlimmerHMM_glimmerT_15586-T1
Valid prediction for pasa_asmbl_48540.p1
Valid prediction for GlimmerHMM_glimmerT_15587-T1
Valid prediction for pasa_asmbl_48546.p1
Valid prediction for GeneMark_model.26226_t
Valid prediction for GlimmerHMM_glimmerT_15589-T1
Valid prediction for pasa_asmbl_48539.p1
Valid prediction for GeneMark_model.26243_t
Valid prediction for GeneMark_model.26249_t
Valid prediction for CodingQuarry_transcript_55016-T1
Valid prediction for CodingQuarry_transcript_55015-T1
Valid prediction for snap_scaffold_6-snap.2011-T1
Valid prediction for GeneMark_model.26232_t
Valid prediction for Augustus_model.g10411.t1
Valid prediction for HiQ_model.g10397.t1
Valid prediction for CodingQuarry_transcript_55013-T1
Valid prediction for pasa_asmbl_48537.p1
Valid prediction for GeneMark_model.26254_t
Valid prediction for HiQ_model.g10399.t1
Valid prediction for GlimmerHMM_glimmerT_15582-T1
Valid prediction for GlimmerHMM_glimmerT_15575-T1
Valid prediction for HiQ_model.g10408.t1
Valid prediction for snap_scaffold_6-snap.2023-T1
Valid prediction for GeneMark_model.26251_t
Valid prediction for HiQ_model.g10405.t1
Valid prediction for GlimmerHMM_glimmerT_15597-T1
Valid prediction for snap_scaffold_6-snap.2007-T1
Valid prediction for snap_scaffold_6-snap.2027-T1
Valid prediction for Augustus_model.g10412.t1
Valid prediction for GeneMark_model.26246_t
Valid prediction for Augustus_model.g10404.t1
Valid prediction for Augustus_model.g10401.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12431, rend_intergenic: 9120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24838, rend_intergenic: 17156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44576, rend_intergenic: 39490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175512
-exon list size: 510


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.6    
14.8    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 12431, rend_intergenic: 9120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24838, rend_intergenic: 17156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44576, rend_intergenic: 39490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 155994 - 175512
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 156516 - 175512
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 157489 - 175512
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 157489 - 171625
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 157489 - 167961
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support